Alpha and Beta Diversity Analysis Tutorial
by Clifton P. Bueno de Mesquita, PhD and Nicholas B. Dragone, PhD
2024-03-19
Fierer Lab, University of Colorado Boulder
Versions:
Version 1: October 2nd 2020 (presented by Cliff to CU Boulder CME)
Version 2: May 26, 2023 (presented by Nick in New Zealand)
This tutorial will cover mctoolsR and some commonly used alpha and beta diversity statistics and plotting. You can do many of the same things with the phyloseq package. We use mctoolsR mainly because it was designed by a former student in the Fierer Lab (Jon Leff) and our dada2 pipeline is set up to export into the format required.
This tutorial was written with R 4.2.3, mctoolsR 0.1.1.9, and dplyr 1.1.3.
Setup
Note the code below uses the example dataset from mctoolsR (https://github.com/leffj/mctoolsr). We will note where you can change the inputs and code to use your own data instead
# R packages required for this tutorial
suppressMessages(library(mctoolsr)) # For inputting, rarefying, filtering, taxonomic analyses
suppressMessages(library(plyr)) # For hulls
suppressMessages(library(tidyverse)) # For data manipulation and plotting
suppressMessages(library(RColorBrewer)) # For color palettes
suppressMessages(library(vegan)) # For alpha and beta diversity analyses
suppressMessages(library(indicspecies)) # For indicator species
suppressMessages(library(car)) # For Levene Test and ANOVA
suppressMessages(library(PMCMRplus)) # For Nemenyi posthoc test
suppressMessages(library(ggh4x)) # For nested facet plots
suppressMessages(library(emmeans)) # For pairwise comparisons
suppressMessages(library(multcomp)) # For automated significant difference letters
suppressMessages(library(zCompositions)) # CLR
suppressMessages(library(compositions)) # Aitchison
suppressMessages(library(reshape2)) # For melting
suppressMessages(library(cowplot)) # For plotting
# Note: This tutorial was run with dplyr 1.1.3. If you are using a newer version of dplyr, you may need to install and load this version using:
#install.packages("dplyr", version='1.1.3')
#library(dplyr)
# If you haven't already installed these packages before, you will need to install them with:
# install.packages()
# For Installing mctoolsR the first time, use:
# install.packages("devtools")
# devtools::install_github("leffj/mctoolsr")
# Custom functions
source("cliffplot_taxa_bars.R")
source("plot_multipatt_asv.R")Loading Data
This loads the mctoolsr example dataset.
# Loading ASV Table
tax_table_fp = system.file('extdata', 'fruits_veggies_taxa_table_wTax.biom',
package = 'mctoolsr')
# Loading mapping file
map_fp = system.file('extdata', 'fruits_veggies_metadata.txt',
package = 'mctoolsr')
# To load YOUR OWN data, replace everything after the "=" with: 'PATH/TO/YOUR_ASV_TABLE_FILE.txt' <- output from dada2 pipeline
# If your files are in your working directly, you do not need to specify the path
# Combine the ASV table and mapping file into an mctoolsR object
input = load_taxa_table(tax_table_fp, map_fp)## 32 samples loaded# If this has worked correctly, you should get a note saying how many samples have been loaded. For the example dataset, this will say "32 samples loaded".Understanding the mctoolsR dataframe
The mctoolsR object is a list with 3 dataframes that can be accessed with $. The dataframes are a sequence table, a mapping file, and a taxonomic file.
# Examine the input dataframes.
head(input$data_loaded) # Rows are OTUs, columns are samples## ProA12 ProA13 ProA14 ProA15 ProA16 ProA33 ProA34 ProA35 ProA36 ProA37
## OTU_2 0 0 0 0 0 0 0 0 2 0
## OTU_3 0 0 0 0 0 1 0 0 0 0
## OTU_12 0 0 0 0 0 0 0 0 0 0
## OTU_13 0 1 0 0 0 0 0 0 0 0
## OTU_20 2 0 0 0 0 0 0 0 0 0
## OTU_25 0 0 0 0 1 0 0 0 0 0
## ProA58 ProA65 ProA66 ProB10 ProB12 ProB33 ProB34 ProB35 ProB36 ProB39
## OTU_2 0 0 0 0 0 0 0 0 0 0
## OTU_3 0 0 0 0 0 0 0 0 0 0
## OTU_12 0 0 0 0 0 0 0 0 0 0
## OTU_13 0 0 0 0 0 0 0 0 0 0
## OTU_20 0 0 0 0 0 0 0 0 0 0
## OTU_25 0 0 0 0 0 0 0 0 0 0
## ProB40 ProB57 ProB58 ProB60 ProB67 ProB70 ProB71 ProB9 ProC36 ProC40
## OTU_2 0 0 0 0 0 0 0 0 0 0
## OTU_3 0 0 0 0 0 0 0 0 0 0
## OTU_12 0 1 0 0 0 0 0 0 0 0
## OTU_13 0 0 0 0 0 0 0 0 0 0
## OTU_20 0 0 0 0 0 0 0 2 0 0
## OTU_25 0 0 0 0 0 0 0 0 0 0
## ProC65 ProC66
## OTU_2 0 0
## OTU_3 0 0
## OTU_12 0 0
## OTU_13 0 0
## OTU_20 0 0
## OTU_25 0 0head(input$taxonomy_loaded) # Rows are OTUs (now ASVs), columns are different taxonomic levels## taxonomy1 taxonomy2 taxonomy3
## OTU_2 k__Bacteria p__Actinobacteria c__Actinobacteria
## OTU_3 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
## OTU_12 k__Bacteria p__Firmicutes c__Bacilli
## OTU_13 Unassigned unclassified unclassified
## OTU_20 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
## OTU_25 Unassigned unclassified unclassified
## taxonomy4 taxonomy5 taxonomy6 taxonomy7
## OTU_2 o__Actinomycetales f__Pseudonocardiaceae g__Amycolatopsis s__
## OTU_3 o__Enterobacteriales f__Enterobacteriaceae g__ s__
## OTU_12 o__Bacillales f__Bacillaceae g__Bacillus s__
## OTU_13 unclassified unclassified unclassified unclassified
## OTU_20 o__Aeromonadales f__Aeromonadaceae g__ s__
## OTU_25 unclassified unclassified unclassified unclassifiedhead(input$map_loaded) # Rows are samples, columns are variables## Sample_type Farm_type Sample_Farming
## ProA12 Mushrooms Conventional Mushrooms_Conventional
## ProA13 Mushrooms Organic Mushrooms_Organic
## ProA14 Mushrooms Organic Mushrooms_Organic
## ProA15 Mushrooms Organic Mushrooms_Organic
## ProA16 Mushrooms Organic Mushrooms_Organic
## ProA33 Strawberries Conventional Strawberries_ConventionalInitial data examinination - reads per sample
One of the first things we want to do is see how many sequences per sample there are.
# This is done by getting the column sums of the sequence table, and we'll sort it too.
sort(colSums(input$data_loaded))## ProA37 ProB70 ProC66 ProB39 ProC40 ProB57 ProA12 ProA58 ProB34 ProC36 ProA65
## 1009 1011 1068 1152 1179 1192 1199 1216 1265 1313 1367
## ProB9 ProB60 ProC65 ProB35 ProB10 ProB67 ProA66 ProB36 ProB71 ProB40 ProA36
## 1371 1395 1409 1492 1599 1611 1614 1642 1745 1771 1802
## ProB58 ProB33 ProA16 ProA35 ProA33 ProB12 ProA13 ProA34 ProA15 ProA14
## 1860 2257 2312 2530 2585 2642 2819 2982 3291 3390# We could also save this as an object and plot it
seqcounts <- as.data.frame(sort(colSums(input$data_loaded)))
# This puts the sample names as row names and the sequence counts column is titled "sort(colSums(input$data_loaded)))
# We'll use the pipeline %>% which is very useful for dataframe management with the dplyr package
# We'll rename the column and make a new column all at once
seqcounts <- as.data.frame(sort(colSums(input$data_loaded))) %>%
rename("seqs" = "sort(colSums(input$data_loaded))") %>%
rownames_to_column(var = "sampleID")
# Now we have a better dataframe with two columns, seqs and sampleID which we can plot
ggplot(seqcounts, aes(reorder(sampleID, seqs, mean), seqs)) + # Dataframe and variables
geom_bar(stat = "identity") + # Type of graph
labs(y = "# Reads", x = "Sample") + # Axes labels
coord_flip() + # Flip axes
theme_classic() + # Plot style. I also use theme_bw() a lot.
theme(axis.text.y = element_text(size = 10)) # Tweak things about text and legend in theme()
Filtering data
We often filter out anything not assigned to a phylum and any control samples. You may also want to do analyses on only a subset of your data, or remove contaminant ASVs that are found in the PCR or extraction blanks. For 16S, at the least filter out mitochondrial, chloroplast, eukaryote DNA, and things unassigned at phylum level. Depending on your samples and analysis goals, you should also consider filtering out extremely rare amplicon sequence variants. Here we will demonstrate removal of what are called “singletons” and “doubletons”, which are individual amplicon sequence variants that only appear once or twice, respectively, in the whole dataset. This is generally recommended.
# Copy the dataset before doing any filtering
input_filt <- input
# For all filtering steps, taxa removed will be output, make note of this for methods section. Also sometimes it will say "Taxa not found" if it is not found. That is an error and the dataset will not be altered. The search is case sensitive.
# This filters out any ASVs from input dataframe ("input_filt") not assigned to a phylum (at taxonomy level 2 = "NA")
input_filt <- filter_taxa_from_input(input_filt,
at_spec_level = 2,
taxa_to_remove = "unclassified") # 978## 978 taxa removed# New versions call it NA
#input_filt <- filter_taxa_from_input(input_filt, at_spec_level = 2, taxa_to_remove = "NA")
# Filtering out mitochondria sequences from the filtered input dataset.
input_filt <- filter_taxa_from_input(input_filt,
taxa_to_remove = "f__mitochondria") # 14 ## 14 taxa removed# New versions call it Mitochondria
#input_filt <- filter_taxa_from_input(input_filt, taxa_to_remove = "Mitochondria")
# Filtering out chloroplast sequences
input_filt <- filter_taxa_from_input(input_filt,
taxa_to_remove = "c__Chloroplast") # 1## 1 taxa removed# New versions call it Chloroplast
#input_filt <- filter_taxa_from_input(input_filt, taxa_to_remove = "Chloroplast")
# Filtering out Eukaryotes
#input_filt <- filter_taxa_from_input(input_filt, taxa_to_remove = "Eukaryota") # 0
# If you want to filter out multiple groups at the same time, you can also do that like this:
# input_filt <- filter_taxa_from_input(input_filt,
# taxa_to_remove = c("Chloroplast",
# "Mitochondria",
# "Eukaryota"))
# However, it's interesting to do it individually to see how much of each DNA category there was!
# Filtering out singletons and doubletons
# First we'll save the ASV IDs of ASVs with less than 3 total counts
singdoub <- data.frame("count" = rowSums(input_filt$data_loaded)) %>%
filter(count < 3) %>%
mutate(ASV = rownames(.))
# Now we'll provide that list of ASV IDs to the taxa_IDs_to_remove argument
input_filt <- filter_taxa_from_input(input_filt,
taxa_IDs_to_remove = singdoub$ASV)## 2091 taxa removed# NOTE: Each line you run updates the input_filt dataset, so be careful, if something goes wrong go back to the start of filtering.
# NOTE: Databases update and sometimes change how Chloroplast, mitochondria, Eukaryotes are named. If you find that you have not filtered anything, search in the taxa table to make sure that you have the right notation. You can do View(input_filt$taxonomy_loaded) and do a quick search.
# NOTE: You can also use taxa_to_keep, specify the taxonomic level with at_spec_level, remove or keep individual ASVs with taxa_IDs_to_keep or taxa_IDs_to_remove, or filter at an abundance threshold.
# In addition to taxonomic filtering, you can filter out samples. For example, let's filter out lettuce samples. We can give a variable name and levels of the variable to filter or keep.
input_filt <- filter_data(input_filt, # provide input_filt again. careful!
filter_cat = "Sample_type",
filter_vals = "Lettuce") # 28 samples remaining (removed 4)## 28 samples remaining# Note: normally after you've filtered and rarefied it's recommended to save the dataset as a .rds file. This ensures you use the same dataset and analysis is reproducible (because rarefaction involves random sampling). Then, if you quit your session but want to reanalyze something, you could just start by reading in your .rds files.
# Lets save the filtered but unrarefied dataset.
saveRDS(input_filt, file = "input_filt.rds")
# You can read it in like this:
input_filt <- readRDS("input_filt.rds")Rarefying data
Moving on, let’s rarefy the data at the lowest count per sample. Sometimes you may want to drop samples and choose a higher number. Rarefaction is one of many ways to normalize data across samples. It has been criticized because you end up throwing away reads. McMurdie and Holmes (2014) argued strongly against it, but the method has since held up to scrutiny (e.g., Weiss et al. 2017 Microbiome, Schloss 2024 mSphere).
# Let's recheck the reads per sample now that we've filtered out a lot of crap.
sort(colSums(input_filt$data_loaded))## ProB70 ProA37 ProC66 ProA12 ProB39 ProC40 ProC36 ProB9 ProB34 ProA65 ProC65
## 949 964 1020 1061 1113 1114 1118 1194 1208 1302 1355
## ProB10 ProB35 ProB71 ProB67 ProA66 ProB36 ProA36 ProB40 ProA16 ProB33 ProB12
## 1383 1458 1463 1491 1514 1585 1696 1743 2056 2111 2165
## ProA35 ProA13 ProA33 ProA34 ProA15 ProA14
## 2378 2390 2428 2790 2828 3000# Rarefy at 949 seqs/sample
set.seed(600) # Set a seed to make this reproducible, although you can also just write to disk and reload the file.
input_filt_rar = single_rarefy(input_filt, 949) # This makes a new mctoolsR dataset called input_filt_rar## 28 samples remaining# The number of samples remaining is stated. Any samples below the threshold get dropped.
# Check seq counts in new dataset
colSums(input_filt_rar$data_loaded) # Good - all 949! It worked.## ProA12 ProA13 ProA14 ProA15 ProA16 ProA33 ProA34 ProA35 ProA36 ProA37 ProA65
## 949 949 949 949 949 949 949 949 949 949 949
## ProA66 ProB10 ProB12 ProB33 ProB34 ProB35 ProB36 ProB39 ProB40 ProB67 ProB70
## 949 949 949 949 949 949 949 949 949 949 949
## ProB71 ProB9 ProC36 ProC40 ProC65 ProC66
## 949 949 949 949 949 949# Save the file. You can reload it with readRDS().
saveRDS(input_filt_rar, file = "input_filt_rar.rds")
input_filt_rar <- readRDS("input_filt_rar.rds")ALPHA DIVERSITY
ASV richness and Shannon diversity. Let’s analyze and graph the number of OTUs (now ASVs) and the Shannon diversity across the sample types.
# First let's get the number of ASVs (richness) per sample and add it to the mapping file
input_filt_rar$map_loaded$rich <- specnumber(input_filt_rar$data_loaded,
MARGIN = 2)
# Now let's get the Shannon diversity index and add it to the mapping file
# Note: Shannon diversity takes into account the ASV richness, as well as evenness
input_filt_rar$map_loaded$shannon <- diversity(input_filt_rar$data_loaded,
index = "shannon",
MARGIN = 2)
# Note: since the data_loaded file has ASVs as rows, MARGIN must be set to 2.Two categories: t-test (parametric) or Wilcoxon Test (non-parametric)
# Two categories example
leveneTest(input_filt_rar$map_loaded$rich ~ input_filt_rar$map_loaded$Farm_type)## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 0.0522 0.8211
## 26# Variance homogeneous (p > 0.05)
shapiro.test(input_filt_rar$map_loaded$rich)##
## Shapiro-Wilk normality test
##
## data: input_filt_rar$map_loaded$rich
## W = 0.97153, p-value = 0.6221# Richness normally distributed (p > 0.05)
t.test(input_filt_rar$map_loaded$rich ~ input_filt_rar$map_loaded$Farm_type)##
## Welch Two Sample t-test
##
## data: input_filt_rar$map_loaded$rich by input_filt_rar$map_loaded$Farm_type
## t = 1.2678, df = 18.164, p-value = 0.2209
## alternative hypothesis: true difference in means between group Conventional and group Organic is not equal to 0
## 95 percent confidence interval:
## -12.72671 51.52671
## sample estimates:
## mean in group Conventional mean in group Organic
## 98.5 79.1# No significant difference in richness among the two categories
# If Levene's Test or Shapiro-Wilk Test p < 0.05, use Wilcoxon Test
wilcox.test(input_filt_rar$map_loaded$rich ~ input_filt_rar$map_loaded$Farm_type)##
## Wilcoxon rank sum exact test
##
## data: input_filt_rar$map_loaded$rich by input_filt_rar$map_loaded$Farm_type
## W = 117, p-value = 0.2079
## alternative hypothesis: true location shift is not equal to 0# Same result
# Box and whisker plot with points
ggplot(input_filt_rar$map_loaded, aes(Farm_type, rich, colour = Farm_type)) +
geom_boxplot(outlier.shape = NA) +
geom_point(size = 3, alpha = 0.5) +
labs(x = "Farm Type", y = "ASV Richness", colour = "Farm Type") +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
# Box and whisker plot with jittered points (geom_jitter instead of geom_point)
ggplot(input_filt_rar$map_loaded, aes(Farm_type, rich, colour = Farm_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
labs(x = "Farm Type", y = "ASV Richness", colour = "Farm Type") +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
# Don't need legend because each category is already clearly labeled
ggplot(input_filt_rar$map_loaded, aes(Farm_type, rich, colour = Farm_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
labs(x = "Farm Type", y = "ASV Richness", colour = "Farm Type") +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
legend.position = "none")
# Change colors to be colorblind friendly (e.g., red and blue is better than red and green)
ggplot(input_filt_rar$map_loaded, aes(Farm_type, rich, colour = Farm_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
labs(x = "Farm Type", y = "ASV Richness", colour = "Farm Type") +
scale_colour_manual(values = c("red", "blue")) +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
legend.position = "none")
# Save plot. This specifies a size and makes it reproducible. pdf default dimensions are in inches. could also use png or jpeg or ggsave. The file will go into working directory unless you specify a different path.
pdf(file = "FarmType.pdf", width = 4, height = 4)
ggplot(input_filt_rar$map_loaded, aes(Farm_type, rich, colour = Farm_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
labs(x = "Farm Type", y = "ASV Richness", colour = "Farm Type") +
scale_colour_manual(values = c("red", "blue")) +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
legend.position = "none")
dev.off()## quartz_off_screen
## 2# Now let's plot Shannon diversity. I cut and pasted the above plot and changed the y input and axis label
ggplot(input_filt_rar$map_loaded, aes(Farm_type, shannon, colour = Farm_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
labs(x = "Farm Type", y = "Shannon diversity", colour = "Farm Type") +
scale_colour_manual(values = c("red", "blue")) +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
legend.position = "none")
Three + categores: ANOVA (parametric) or Kruskal-Wallis (non-parametric)
# Three category example
leveneTest(input_filt_rar$map_loaded$rich ~ input_filt_rar$map_loaded$Sample_type)## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 2 2.3697 0.1142
## 25# Variance homogeneous (p > 0.05)
m <- aov(input_filt_rar$map_loaded$rich ~ input_filt_rar$map_loaded$Sample_type)
shapiro.test(m$residuals)##
## Shapiro-Wilk normality test
##
## data: m$residuals
## W = 0.95207, p-value = 0.2232# Residuals normally distributed (p > 0.05)
# Note: Here we test the assumption that the residuals (not the data itself) are normally distributed
# Other diagnostics - learn more here (https://data.library.virginia.edu/diagnostic-plots/)
# Note: R markdown will plot all 4 diagnostic plots. If not in R markdown, click in the console and hit Return to see each diagnostic plot.
plot(m) 
# Check the model results.
summary(m)## Df Sum Sq Mean Sq F value Pr(>F)
## input_filt_rar$map_loaded$Sample_type 2 16732 8366 8.705 0.00135 **
## Residuals 25 24025 961
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1# Significant effect. Run posthoc test to see which groups are different from each other.
# Mushrooms different from spinach and strawberries. No diff between spinach and strawberries
TukeyHSD(m)## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = input_filt_rar$map_loaded$rich ~ input_filt_rar$map_loaded$Sample_type)
##
## $`input_filt_rar$map_loaded$Sample_type`
## diff lwr upr p adj
## Spinach-Mushrooms -43.96429 -83.92742 -4.00115 0.0290426
## Strawberries-Mushrooms -57.48077 -92.17849 -22.78305 0.0010087
## Strawberries-Spinach -13.51648 -49.71596 22.68299 0.6267806# If Levene's Test or Shapiro-Wilk Test p < 0.05, use Krukal-Wallis Test
# Note: The Nemenyi test only accepts a factor independent variable so we add as.factor() to the independent variable.
kruskal.test(input_filt_rar$map_loaded$rich ~ input_filt_rar$map_loaded$Sample_type)##
## Kruskal-Wallis rank sum test
##
## data: input_filt_rar$map_loaded$rich by input_filt_rar$map_loaded$Sample_type
## Kruskal-Wallis chi-squared = 9.2183, df = 2, p-value = 0.00996# Significant effect. (agrees with ANOVA). Run posthoc.
kwAllPairsNemenyiTest(input_filt_rar$map_loaded$rich ~ as.factor(input_filt_rar$map_loaded$Sample_type))##
## Pairwise comparisons using Tukey-Kramer-Nemenyi all-pairs test with Tukey-Dist approximation## data: input_filt_rar$map_loaded$rich by as.factor(input_filt_rar$map_loaded$Sample_type)## Mushrooms Spinach
## Spinach 0.0797 -
## Strawberries 0.0086 0.8879##
## P value adjustment method: single-step## alternative hypothesis: two.sided# Similar result, but spinach/mushroom different now only marginal.
# Use ANOVA result if assumptions passed because there is more power and data aren't rank transformed, which is a loss of information.
# Plot. Just copy the previous plot, change the variable name and the colour argument!
# Here we'll try the viridis palette.
ggplot(input_filt_rar$map_loaded, aes(Sample_type, rich, colour = Sample_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
labs(x = "Sample Type", y = "ASV Richness", colour = "Farm Type") +
scale_colour_viridis_d() +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
legend.position = "none")
# Now, since there was a significant difference, let's add some letter text. We'll make a new dataframe containing coordinates for the letters. Groups with different letters are significantly different. So it should be a b b. We set y to 180 to be above the maximum ASV richness.
label_df <- data.frame(x = c("Mushrooms", "Spinach", "Strawberries"),
y = c(180, 180, 180),
label = c("a", "b", "b"))
# Plot with added geom_text
ggplot(input_filt_rar$map_loaded, aes(Sample_type, rich, colour = Sample_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
geom_text(data = label_df, aes(x, y, label = label), size = 5, inherit.aes = F) +
labs(x = "Sample Type", y = "ASV Richness", colour = "Farm Type") +
scale_colour_viridis_d() +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
legend.position = "none")
Multipanel plot.
What one might want to show as, say, Figure 1 in a paper for a nice overview of the microbial communities, could be a multipanel plot with both ASV richness and Shannon diversity.
Let’s use an automated method for generating the significant difference letters, and then “melt” the data into long format for multipanel plotting
## Stats for rich and Shannon using ANOVA and emmeans and cld.
m1 <- aov(rich ~ Sample_type, data = input_filt_rar$map_loaded)
t1 <- emmeans(object = m1, specs = "Sample_type") %>%
cld(object = ., adjust = "Tukey", Letters = letters, alpha = 0.05) %>%
mutate(name = "rich",
y = 180)## Note: adjust = "tukey" was changed to "sidak"
## because "tukey" is only appropriate for one set of pairwise comparisonsm2 <- aov(shannon ~ Sample_type, data = input_filt_rar$map_loaded)
t2 <- emmeans(object = m2, specs = "Sample_type") %>%
cld(object = ., adjust = "Tukey", Letters = letters, alpha = 0.05) %>%
mutate(name = "shannon",
y = 5)## Note: adjust = "tukey" was changed to "sidak"
## because "tukey" is only appropriate for one set of pairwise comparisons# Note: The sidak note is fine. It's still a Tukey posthoc test, just with sidak adjustment.
# Combine the labels
label_df <- rbind(t1, t2)
# Set names for the facet strips
facet_df <- c("rich" = "(a) Richness",
"shannon" = "(b) Shannon")
# Make the data long format
alpha_long <- input_filt_rar$map_loaded %>%
pivot_longer(cols = c("rich", "shannon"))
# This will put the richness and Shannon values into a column named "value"
# It will make a new column ("name") which maps the values to either richness or shannon
# Plot using facet_wrap to make the two panels. We use scales = "free_y" to let the y-axis scale vary among the two panels.
ggplot(alpha_long, aes(Sample_type, value, colour = Sample_type)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(size = 3, alpha = 0.5) +
geom_text(data = label_df,
aes(Sample_type, y, label = str_trim(.group)),
size = 5, inherit.aes = F) +
labs(x = "Sample Type", y = "ASV Richness", colour = "Farm Type") +
scale_colour_viridis_d() +
facet_wrap(~name, ncol = 2, scales = "free_y", labeller = as_labeller(facet_df)) +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
strip.text = element_text(size = 18),
legend.position = "none")
BETA DIVERSITY
Now let’s assess differences in entire community composition among sample types. We will calculate Aitchison and Bray-Curtis dissimilarity, plot ordinations, and run multivariate stats. The conventional method has long been to calculate a Bray-Curtis dissimilarity matrix and then plot a PCoA or NMDS. We will first do these and then go over a newer method that is now preferred by many (e.g., Gloor et al. 2017 Frontiers in Microbiology).
Bray-Curtis and NMDS
# Calculate dissimilarity matrix
dm <- calc_dm(input_filt_rar$data_loaded)
# NOTE: calc_dm uses Bray-Curtis by default. Can change to others using method=type_of_function in the script
# Let's calculate an ordination from the distance matrix
ord <- calc_ordination(dm, 'nmds')## Run 0 stress 0.1045557
## Run 1 stress 0.1227621
## Run 2 stress 0.1050761
## Run 3 stress 0.1045555
## ... New best solution
## ... Procrustes: rmse 0.0001632318 max resid 0.0006795909
## ... Similar to previous best
## Run 4 stress 0.1199644
## Run 5 stress 0.124056
## Run 6 stress 0.1050761
## Run 7 stress 0.1337521
## Run 8 stress 0.1199642
## Run 9 stress 0.1231582
## Run 10 stress 0.1240559
## Run 11 stress 0.1352062
## Run 12 stress 0.1199643
## Run 13 stress 0.1045556
## ... Procrustes: rmse 0.0003409372 max resid 0.001420896
## ... Similar to previous best
## Run 14 stress 0.1358001
## Run 15 stress 0.1045555
## ... Procrustes: rmse 0.0003152746 max resid 0.001313637
## ... Similar to previous best
## Run 16 stress 0.1249811
## Run 17 stress 0.1045555
## ... Procrustes: rmse 0.0003039307 max resid 0.001265566
## ... Similar to previous best
## Run 18 stress 0.1045556
## ... Procrustes: rmse 0.0003394067 max resid 0.001413822
## ... Similar to previous best
## Run 19 stress 0.1240559
## Run 20 stress 0.1240559
## *** Best solution repeated 5 times# NOTE: You can also run pcoa and others by changing the code above from NMDS
# Now plot the ordination using the default mctoolsR function.
plot_ordination(input_filt_rar, ord, 'Sample_type', 'Farm_type', hulls = TRUE)## Warning: `do_()` was deprecated in dplyr 0.7.0.
## ℹ Please use `do()` instead.
## ℹ See vignette('programming') for more help
## ℹ The deprecated feature was likely used in the mctoolsr package.
## Please report the issue at <https://github.com/leffj/mctoolsr/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: `group_by_()` was deprecated in dplyr 0.7.0.
## ℹ Please use `group_by()` instead.
## ℹ See vignette('programming') for more help
## ℹ The deprecated feature was likely used in the mctoolsr package.
## Please report the issue at <https://github.com/leffj/mctoolsr/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
#this is a nice thing to do at the start of an analysis to see what your data is doing
# NOTE: plot_ordination is a good way to quickly plot data. However, if you want to do more complicated edits to a plot, you should save the ordination values from the calc_ordination() step as a dataframe and plot in ggplot as shown below.Bray-Curtis and PCoA
This does basically the same thing as above, but it uses Principle Coordinates Analysis (PCoA) instead of Non-metric multidimensional scaling (NMDS). It is worth seeing that you can do basically the same thing using two different codes and is a good check of the consistency of the ordination. We also demonstrate saving the ordination scores and making a custom ggplot figure rather than relying on the default mctoolsR function.
# Bray-Curtis dissimilarity matrix. Note: By default the data are square-root transformed.
bc <- calc_dm(input_filt_rar$data_loaded)
# Principle Coordinates Analysis (PCoA)
pcoa <- cmdscale(bc, k = nrow(input_filt_rar$map_loaded) - 1, eig = T)
# Variation Explained
eigenvals(pcoa)/sum(eigenvals(pcoa)) # 23.3, 16.6 % variation explained## [1] 0.23299874 0.16603055 0.12452778 0.08016005 0.04836278 0.04258608
## [7] 0.03804139 0.03274082 0.02968823 0.02785019 0.02095102 0.02045540
## [13] 0.01652821 0.01518103 0.01370175 0.01275645 0.01188354 0.01128799
## [19] 0.00957814 0.00922398 0.00795294 0.00732115 0.00670822 0.00555404
## [25] 0.00428130 0.00314296 0.00050527 0.00000000# Make axis labels with % variation explained rounded to 1 digit.
pcoaA1 <- paste("PC1: ", round((eigenvals(pcoa)/sum(eigenvals(pcoa)))[1]*100, 1), "%")
pcoaA2 <- paste("PC2: ", round((eigenvals(pcoa)/sum(eigenvals(pcoa)))[2]*100, 1), "%")
# Save Axis 1 and 2 scores to the mapping file
input_filt_rar$map_loaded$Axis01 <- scores(pcoa)[,1]
input_filt_rar$map_loaded$Axis02 <- scores(pcoa)[,2]
# Function for making a convex hull
find_hull <- function(df) df[chull(df$Axis01, df$Axis02),]
# Calculate hulls and save to dataframe
micro.hulls <- ddply(input_filt_rar$map_loaded, c("Sample_type", "Farm_type"), find_hull)
# Plot
ggplot(input_filt_rar$map_loaded, aes(Axis01, Axis02, colour = Sample_type, shape = Farm_type)) +
geom_polygon(data = micro.hulls, aes(colour = Sample_type, fill = Sample_type),
alpha = 0.1, show.legend = F) +
geom_point(size = 2, alpha = 0.5) +
labs(x = pcoaA1,
y = pcoaA2,
colour = "Food",
shape = "Farm") +
scale_colour_viridis_d() +
scale_fill_viridis_d() +
theme_bw() +
theme(legend.position = "right",
axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
Aitchison Matrix and PCA
Some authors (e.g., Gloor et al. 2017) have argued for using Aitchison’s distance instead of Bray-Curtis dissimilarity. Then, a PCA instead of PCoA is performed. Instead of using rarefied data, we will use our unrarefied (but filtered) dataset and perform a center log ratio transformation.
# First perform zero replacement and center log ratio (CLR) transformation. Use filtered but unrarefied data for this ("input_filt").
otu_czm <- cmultRepl(t(input_filt$data_loaded), label = 0, method = "CZM")## Warning in cmultRepl(t(input_filt$data_loaded), label = 0, method = "CZM"): Column 1 containing more than 80% zeros/unobserved values was deleted (pre-check out using function zPatterns/modify threshold using argument z.warning).
## Column 2 containing more than 80% zeros/unobserved values was deleted (pre-check out using function zPatterns/modify threshold using argument z.warning).
## Column 3 containing more than 80% zeros/unobserved values was deleted (pre-check out using function zPatterns/modify threshold using argument z.warning).
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## Column 63 containing more than 80% zeros/unobserved values was deleted (pre-check out using function zPatterns/modify threshold using arg## Warning in cmultRepl(t(input_filt$data_loaded), label = 0, method = "CZM"): Row 3 containing more than 80% zeros/unobserved values was deleted (pre-check out using function zPatterns/modify threshold using argument z.warning).
## Row 17 containing more than 80% zeros/unobserved values was deleted (pre-check out using function zPatterns/modify threshold using argument z.warning).
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## Row 26 containing more than 80% zeros/unobserved values was deleted (pre-check out using function zPatterns/modify threshold using argument z.warning).## No. adjusted imputations: 84otu_clr <- clr(otu_czm)
aclr <- compositions::dist(otu_clr)
# Filter dropped samples
# Columns and rows containing more than 80% zeros/unobserved values were deleted
# This is the bad thing about this method. We have now lost some samples and ASVs.
# You can also avoid this by adjusting the z.warning.
# Here we just proceed with the default.
dim(t(input_filt$data_loaded)) # 28 samples, 933 ASVs## [1] 28 933dim(otu_czm) # 23 samples, 144 ASVs## [1] 23 144# Make a sampleID column
input_filt$map_loaded$sampleID <- rownames(input_filt$map_loaded)
# Filter out sampleIDs not in the CLR dataset. Save as new mctoolsR object.
input_filt_clr <- filter_data(input_filt,
filter_cat = "sampleID",
keep_vals = rownames(otu_czm))## 23 samples remaining# PCA (principle components analysis)
d.pcx <- prcomp(aclr)
# % variation explained
d.mvar <- sum(d.pcx$sdev^2)
# Make axes labels with % variation explained
PC1 <- paste("PC1: ", round((sum(d.pcx$sdev[1]^2)/d.mvar)*100, 1), "%")
PC2 <- paste("PC2: ", round((sum(d.pcx$sdev[2]^2)/d.mvar)*100, 1), "%")
# Save scores to map_loaded dataframe
input_filt_clr$map_loaded$Axis01 <- d.pcx$x[,1]
input_filt_clr$map_loaded$Axis02 <- d.pcx$x[,2]
# Transform the scores
input_filt_clr$map_loaded$Axis01 <- input_filt_clr$map_loaded$Axis01/sqrt(sum((input_filt_clr$map_loaded$Axis01 - mean(input_filt_clr$map_loaded$Axis01))^2))
input_filt_clr$map_loaded$Axis02 <- input_filt_clr$map_loaded$Axis02/sqrt(sum((input_filt_clr$map_loaded$Axis02 - mean(input_filt_clr$map_loaded$Axis02))^2))
# Calculate hulls
micro.hulls <- ddply(input_filt_clr$map_loaded, c("Sample_type", "Farm_type"), find_hull)
# Plot
ggplot(input_filt_clr$map_loaded, aes(Axis01, Axis02, colour = Sample_type, shape = Farm_type)) +
geom_polygon(data = micro.hulls, aes(colour = Sample_type, fill = Sample_type),
alpha = 0.1, show.legend = F) +
geom_point(size = 2, alpha = 0.5) +
labs(x = PC1,
y = PC1,
colour = "Food",
shape = "Farm") +
scale_colour_viridis_d() +
scale_fill_viridis_d() +
theme_bw() +
theme(legend.position = "right",
axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
# Note: This is very consistent with the Bray-Curtis and PCoA.PERMANOVA, PERMDISP
Now we need to run some statisitcs to test for differences in community composition among treatments as well as homogeneity of dispersion within treatments.
# PERMANOVA (multivariate version of ANOVA)
set.seed(1223) # To make reproducible
m <- adonis2(bc ~ input_filt_rar$map_loaded$Sample_type*input_filt_rar$map_loaded$Farm_type)
m## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = bc ~ input_filt_rar$map_loaded$Sample_type * input_filt_rar$map_loaded$Farm_type)
## Df
## input_filt_rar$map_loaded$Sample_type 2
## input_filt_rar$map_loaded$Farm_type 1
## input_filt_rar$map_loaded$Sample_type:input_filt_rar$map_loaded$Farm_type 2
## Residual 22
## Total 27
## SumOfSqs
## input_filt_rar$map_loaded$Sample_type 3.4460
## input_filt_rar$map_loaded$Farm_type 0.4967
## input_filt_rar$map_loaded$Sample_type:input_filt_rar$map_loaded$Farm_type 0.8515
## Residual 4.7867
## Total 9.5809
## R2
## input_filt_rar$map_loaded$Sample_type 0.35968
## input_filt_rar$map_loaded$Farm_type 0.05184
## input_filt_rar$map_loaded$Sample_type:input_filt_rar$map_loaded$Farm_type 0.08887
## Residual 0.49961
## Total 1.00000
## F
## input_filt_rar$map_loaded$Sample_type 7.9190
## input_filt_rar$map_loaded$Farm_type 2.2828
## input_filt_rar$map_loaded$Sample_type:input_filt_rar$map_loaded$Farm_type 1.9567
## Residual
## Total
## Pr(>F)
## input_filt_rar$map_loaded$Sample_type 0.001
## input_filt_rar$map_loaded$Farm_type 0.013
## input_filt_rar$map_loaded$Sample_type:input_filt_rar$map_loaded$Farm_type 0.015
## Residual
## Total
##
## input_filt_rar$map_loaded$Sample_type ***
## input_filt_rar$map_loaded$Farm_type *
## input_filt_rar$map_loaded$Sample_type:input_filt_rar$map_loaded$Farm_type *
## Residual
## Total
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1# Significant effects of sample type, farm type and interaction.
# What about pairwise PERMANOVA? This is similar to a Tukey posthoc an an ANOVA.
# Grouping variable must be a factor
input_filt_rar$map_loaded$Sample_type <- as.factor(input_filt_rar$map_loaded$Sample_type)
set.seed(1223)
m_pw <- calc_pairwise_permanovas(bc, input_filt_rar$map_loaded, "Sample_type")## 'adonis' will be deprecated: use 'adonis2' instead
## 'adonis' will be deprecated: use 'adonis2' instead
## 'adonis' will be deprecated: use 'adonis2' insteadm_pw # Each group is significantly different from the other.## X1 X2 R2 pval pvalBon pvalFDR
## 1 Mushrooms Spinach 0.3838730 0.001 0.003 0.002
## 2 Mushrooms Strawberries 0.2794695 0.001 0.003 0.002
## 3 Spinach Strawberries 0.2449625 0.001 0.003 0.002# PERMDISP (multivariate version of Levene's Test)
m1 <- betadisper(bc, input_filt_rar$map_loaded$Sample_type)
anova(m1) # Dispersion different## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 2 0.146182 0.073091 20.36 5.663e-06 ***
## Residuals 25 0.089748 0.003590
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1m2 <- betadisper(bc, input_filt_rar$map_loaded$Farm_type)
anova(m2) # Dispersion homogeneous## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 1 0.01824 0.0182398 2.586 0.1199
## Residuals 26 0.18339 0.0070533m3 <- betadisper(bc, input_filt_rar$map_loaded$Sample_Farming)
anova(m3) # Dispersion different## Analysis of Variance Table
##
## Response: Distances
## Df Sum Sq Mean Sq F value Pr(>F)
## Groups 5 0.20207 0.040414 4.2705 0.007261 **
## Residuals 22 0.20820 0.009464
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1# Let's add the centroids to our PCoA plot.
# Centroids are contained here:
m3$centroids## PCoA1 PCoA2 PCoA3 PCoA4
## Mushrooms_Conventional -0.38575907 0.03883206 -0.01061624 -0.262371754
## Mushrooms_Organic -0.48736641 0.06046629 0.04946520 0.269786066
## Spinach_Conventional 0.14842443 -0.32777104 0.11029008 0.035217506
## Spinach_Organic 0.04248558 -0.35249459 0.16583474 -0.049806583
## Strawberries_Conventional 0.21382989 0.06724047 -0.11846836 0.005091353
## Strawberries_Organic 0.18535239 0.35687881 0.03360756 0.017843245
## PCoA5 PCoA6 PCoA7 PCoA8
## Mushrooms_Conventional 0.007037599 0.010727625 0.01413591 0.024114352
## Mushrooms_Organic 0.045091973 -0.008263158 0.01704842 -0.018779568
## Spinach_Conventional 0.036795703 0.044499909 -0.10744589 0.057006371
## Spinach_Organic -0.193589544 -0.136837666 0.09354917 0.009955471
## Strawberries_Conventional 0.067823499 0.022776835 0.06926734 -0.032714414
## Strawberries_Organic -0.134110306 -0.046712483 -0.12714419 -0.016102192
## PCoA9 PCoA10 PCoA11 PCoA12
## Mushrooms_Conventional -0.006914227 0.11702031 -0.02698791 0.006258975
## Mushrooms_Organic -0.007050640 -0.05766898 0.02147945 0.003249889
## Spinach_Conventional -0.021404063 0.02237317 0.01008622 0.029165971
## Spinach_Organic 0.044903875 -0.07110968 -0.03133753 -0.042587096
## Strawberries_Conventional -0.034957121 -0.01011234 -0.01527359 -0.016338512
## Strawberries_Organic 0.040758276 0.02419418 0.03612080 0.024481711
## PCoA13 PCoA14 PCoA15 PCoA16
## Mushrooms_Conventional -0.003960223 -0.006730886 0.0009626401 0.005563734
## Mushrooms_Organic 0.008540610 -0.005277012 0.0031150796 -0.005888112
## Spinach_Conventional 0.003465431 -0.036029157 0.0027143436 0.011429085
## Spinach_Organic -0.026612229 0.091813095 -0.0083078665 -0.045376336
## Strawberries_Conventional -0.011999039 0.008081568 -0.0032411634 -0.000675784
## Strawberries_Organic 0.018272143 0.009819088 0.0021547380 -0.008962818
## PCoA17 PCoA18 PCoA19 PCoA20
## Mushrooms_Conventional 0.005720225 0.010544143 -2.115485e-05 -0.005627660
## Mushrooms_Organic 0.005028246 -0.008982367 6.953284e-03 0.010701290
## Spinach_Conventional -0.007022220 0.015678956 6.312013e-03 0.013330204
## Spinach_Organic 0.034767559 -0.033496916 -2.966745e-02 -0.003740187
## Strawberries_Conventional -0.004949216 -0.008183587 4.035726e-03 -0.009357069
## Strawberries_Organic 0.012706439 0.009206557 -1.034710e-02 0.015367916
## PCoA21 PCoA22 PCoA23 PCoA24
## Mushrooms_Conventional 0.0056129083 0.009042009 0.0009245449 -0.006018883
## Mushrooms_Organic -0.0072696619 0.008235559 0.0006905917 -0.004527507
## Spinach_Conventional -0.0097473366 -0.002722524 0.0052384694 0.019420532
## Spinach_Organic 0.0176757805 0.007474991 -0.0497621993 -0.021066493
## Strawberries_Conventional -0.0007101365 0.005141392 -0.0018611850 -0.001863626
## Strawberries_Organic -0.0027793625 -0.011338879 0.0074435442 -0.006957195
## PCoA25 PCoA26 PCoA27
## Mushrooms_Conventional -0.0004846792 -0.001620327 0.0002772015
## Mushrooms_Organic 0.0024893278 0.001371614 -0.0001481248
## Spinach_Conventional 0.0012518818 0.003043980 0.0003390877
## Spinach_Organic -0.0028499057 0.010268601 -0.0029428609
## Strawberries_Conventional -0.0037592705 -0.001903678 0.0030039133
## Strawberries_Organic 0.0117045356 0.002096310 -0.0060292168# First make a clean data frame with %>%
centroids <- as.data.frame(m3$centroids) %>%
dplyr::select(PCoA1, PCoA2) %>%
rename(Axis01 = PCoA1,
Axis02 = PCoA2) %>%
rownames_to_column(var = "Sample_Farming") %>%
separate(Sample_Farming, into = c("Sample_type", "Farm_type"), sep = "_")
# Remake the hulls
micro.hulls <- ddply(input_filt_rar$map_loaded, c("Sample_type", "Farm_type"), find_hull)
# Plot
ggplot(input_filt_rar$map_loaded, aes(Axis01, Axis02, colour = Sample_type, shape = Farm_type)) +
geom_polygon(data = micro.hulls, aes(colour = Sample_type, fill = Sample_type),
alpha = 0.1, show.legend = F) +
geom_point(size = 2, alpha = 0.5) +
geom_point(data = centroids, size = 4) +
labs(x = pcoaA1,
y = pcoaA2,
colour = "Food",
shape = "Farm") +
scale_colour_viridis_d() +
scale_fill_viridis_d() +
theme_bw() +
theme(legend.position = "right",
axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
Multipanel PCoA plots
As a bonus, let’s make a multipanel PCoA plot. This can be really useful if you have a 16S dataset and an 18S or ITS dataset, and you want to show both side by side. In this case, let’s just make another PCoA with the same dataset. Let’s just use the original unfiltered unrarefied dataset. This will also show us how filtering and rarefying affected the analysis. Let’s remove lettuce though so the factor levels are the same.
# Bray-Curtis Matrix
input_nolet <- filter_data(input,
filter_cat = "Sample_type",
filter_vals = "Lettuce") # 28 samples remaining (removed 4)## 28 samples remainingbc2 <- calc_dm(input_nolet$data_loaded)
# Principle Coordinates Analysis (PCoA)
pcoa2 <- cmdscale(bc2, k = nrow(input_nolet$map_loaded) - 1, eig = T)
# Variation Explained
eigenvals(pcoa2)/sum(eigenvals(pcoa2)) # 18.0, 13.9 % variation explained## [1] 0.18038793 0.13909543 0.10727935 0.06995555 0.04782424 0.04251012
## [7] 0.04037428 0.03387551 0.03344651 0.03081348 0.02753299 0.02585268
## [13] 0.02451780 0.02207721 0.02006282 0.01860184 0.01722138 0.01578966
## [19] 0.01516671 0.01493567 0.01433535 0.01329144 0.01264790 0.01010843
## [25] 0.00947210 0.00716815 0.00565548 0.00000000# Save Axis 1 and 2 to the mapping file
input_nolet$map_loaded$Axis01 <- scores(pcoa2)[,1]
input_nolet$map_loaded$Axis02 <- scores(pcoa2)[,2]
# Now we need to combine the two datasets. We'll stack them on top of each other with rbind. In order to do this, the columns must match. Right now we have an extra columns in input_filt_rar$map_loaded (e.g., rich and shannon). To be sure let's just select the columns we need from each and then stack. We also need to add a column stating the dataset - we'll use this as a variable to specify the panels.
df1 <- input_filt_rar$map_loaded %>%
dplyr::select(Sample_type, Farm_type, Sample_Farming, Axis01, Axis02) %>%
mutate(Dataset = "a) Rarefied, filtered")
df2 <- input_nolet$map_loaded %>%
dplyr::select(Sample_type, Farm_type, Sample_Farming, Axis01, Axis02) %>%
mutate(Dataset = "b) Unrarefied, unfiltered")
df3 <- rbind(df1, df2)
# Now we'll make a label data frame for the % variation explained. To get the right x and y values, check the range of axes values. You can also plot, adjust, and replot.
range(df1$Axis01)## [1] -0.5274262 0.3176546range(df2$Axis01)## [1] -0.4816218 0.2969321range(df1$Axis02)## [1] -0.3619609 0.4673646range(df2$Axis02)## [1] -0.3221893 0.4481281label_df2 <- data.frame(x = c(-0.35, -0.35),
y = c(-0.35, -0.35),
Dataset = c("a) Rarefied, filtered", "b) Unrarefied, unfiltered"),
label = c("23.3%, 16.6%", "18.0%, 13.9%"))
# Now we need to make new hulls. The hulls will be the same as before but we'll add Dataset as a variable.
micro.hulls2 <- ddply(df3, c("Dataset","Sample_type","Farm_type"), find_hull)
ggplot(df3, aes(Axis01, Axis02, colour = Sample_type, shape = Farm_type)) +
geom_polygon(data = micro.hulls2, aes(colour = Sample_type, fill = Sample_type),
alpha = 0.1, show.legend = F) +
geom_point(size = 2, alpha = 0.5) +
geom_text(data = label_df2, aes(x, y, label = label), size = 3, inherit.aes = F) +
labs(x = "PC1",
y = "PC2",
colour = "Food",
shape = "Farm") +
scale_colour_viridis_d() +
scale_fill_viridis_d() +
facet_wrap(~ Dataset) + # We did not define a scales argument, so axes have the same scales
theme_bw() +
theme(legend.position = "right",
axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14),
strip.text = element_text(size = 12))
# The overall trends are the same but there were some minor shifts. Also the rarefied/filtered dataset gets more % variation explained by the first 2 axes.Hierarchical Clustering
Another option to examine community composition among your samples and treatments is to see how they cluster. You can already see how they cluster in the ordination plots, but this is another method that can be used.
# Cluster according to Ward's D2. There are other methods available.
# The input is a dissimilarity matrix. Here we'll use the Bray-Curtis one.
h <- hclust(bc)
# The default plot of the saved hclust object will immediately give you an overview of how the samples cluster.
# There are ways to clean up these plots and make them pretty and color by treatments but that won't be covered here.
plot(h)
TAXONOMIC ANALYSIS
Indicator Taxa
Let’s first check for indicator taxa for our grouping variables. We will try two methods, SIMPER and MULTIPATT. SIMPER will list how much each ASV contributes to dissimilarity among groups. MULTIPATT will list indicators for each individual group as well as combinations of groups. These methods use a large amount of computer memory and can sometimes take a while or max out your computer, depending on the dataset size. It will run faster/better on a server or if you just run it on the most abundant taxa instead of tens of thousands of ASVs. In this case, this is a simple dataset and we won’t have any problems.
# SIMPER (list how much each ASV contributes to dissimilarity among groups)
sim <- simper(t(input_filt_rar$data_loaded),
input_filt_rar$map_loaded$Sample_type)
s <- summary(sim)
# Let's look at the top 5 contributing to dissimilarity between mushrooms and strawberries/spinach
head(s$Mushrooms_Strawberries, n = 5)## average sd ratio ava avb cumsum p
## OTU_5339 0.15510254 0.15712746 0.9871129 0.000 294.38461538 0.1579854 0.034
## OTU_1763 0.07767285 0.10876583 0.7141292 0.750 147.53846154 0.2371020 0.193
## OTU_7240 0.07004843 0.04265811 1.6420893 133.875 0.92307692 0.3084524 0.001
## OTU_6975 0.05174982 0.05932183 0.8723571 3.625 101.30769231 0.3611641 1.000
## OTU_8870 0.04310712 0.06974072 0.6181054 81.875 0.07692308 0.4050725 0.001head(s$Mushrooms_Spinach, n = 5)## average sd ratio ava avb cumsum p
## OTU_6975 0.20191367 0.06950675 2.9049506 3.625 386.85714 0.2172342 0.001
## OTU_6245 0.06529429 0.04392433 1.4865178 5.500 129.42857 0.2874828 0.001
## OTU_7240 0.05378782 0.04099386 1.3120945 133.875 44.57143 0.3453519 0.021
## OTU_8870 0.04277999 0.06993490 0.6117117 81.875 1.00000 0.3913778 0.030
## OTU_9155 0.03562961 0.05730298 0.6217759 67.625 0.00000 0.4297109 0.014# average is the proportion contribution, cumsum is cumulative, ava and avb are mean sequence abundances per group.
# in this case it looks like the top 5 ASVs are expalining a lot of the difference (~40%)
# MULTIPATT (list ASVs associated with each group)
# Groups can be individual treatments or groups of treatments
set.seed(1223) # For reproducability
mp <- multipatt(t(input_filt_rar$data_loaded),
input_filt_rar$map_loaded$Sample_type,
func = "IndVal.g",
control = how(nperm=999))
summary(mp)##
## Multilevel pattern analysis
## ---------------------------
##
## Association function: IndVal.g
## Significance level (alpha): 0.05
##
## Total number of species: 888
## Selected number of species: 204
## Number of species associated to 1 group: 191
## Number of species associated to 2 groups: 13
##
## List of species associated to each combination:
##
## Group Mushrooms #sps. 107
## stat p.value
## OTU_7703 0.999 0.001 ***
## OTU_4891 0.935 0.001 ***
## OTU_6190 0.935 0.001 ***
## OTU_7523 0.935 0.001 ***
## OTU_9155 0.935 0.001 ***
## OTU_8870 0.929 0.004 **
## OTU_3033 0.877 0.001 ***
## OTU_3636 0.866 0.001 ***
## OTU_8177 0.866 0.001 ***
## OTU_12181 0.866 0.001 ***
## OTU_8653 0.858 0.001 ***
## OTU_3785 0.846 0.002 **
## OTU_1478 0.791 0.001 ***
## OTU_1527 0.791 0.001 ***
## OTU_1730 0.791 0.004 **
## OTU_3432 0.791 0.002 **
## OTU_4062 0.791 0.001 ***
## OTU_6747 0.791 0.002 **
## OTU_8874 0.791 0.002 **
## OTU_9608 0.791 0.002 **
## OTU_10514 0.791 0.001 ***
## OTU_11482 0.791 0.002 **
## OTU_11952 0.791 0.002 **
## OTU_12614 0.791 0.001 ***
## OTU_6760 0.790 0.002 **
## OTU_5927 0.779 0.011 *
## OTU_2395 0.776 0.002 **
## OTU_13366 0.742 0.006 **
## OTU_995 0.707 0.001 ***
## OTU_1295 0.707 0.004 **
## OTU_2241 0.707 0.007 **
## OTU_2402 0.707 0.006 **
## OTU_2428 0.707 0.004 **
## OTU_2797 0.707 0.006 **
## OTU_3563 0.707 0.004 **
## OTU_3804 0.707 0.005 **
## OTU_4354 0.707 0.006 **
## OTU_4456 0.707 0.006 **
## OTU_4688 0.707 0.007 **
## OTU_5186 0.707 0.006 **
## OTU_7569 0.707 0.004 **
## OTU_9903 0.707 0.003 **
## OTU_10146 0.707 0.006 **
## OTU_10284 0.707 0.008 **
## OTU_10759 0.707 0.006 **
## OTU_10769 0.707 0.006 **
## OTU_11299 0.707 0.006 **
## OTU_12424 0.707 0.005 **
## OTU_12968 0.707 0.004 **
## OTU_5354 0.697 0.009 **
## OTU_10979 0.690 0.021 *
## OTU_9742 0.644 0.041 *
## OTU_229 0.612 0.031 *
## OTU_242 0.612 0.028 *
## OTU_294 0.612 0.026 *
## OTU_378 0.612 0.028 *
## OTU_860 0.612 0.023 *
## OTU_1029 0.612 0.028 *
## OTU_1160 0.612 0.024 *
## OTU_1542 0.612 0.025 *
## OTU_1702 0.612 0.024 *
## OTU_1709 0.612 0.028 *
## OTU_1931 0.612 0.025 *
## OTU_2039 0.612 0.028 *
## OTU_2270 0.612 0.034 *
## OTU_2608 0.612 0.028 *
## OTU_2798 0.612 0.027 *
## OTU_2900 0.612 0.028 *
## OTU_2953 0.612 0.029 *
## OTU_3052 0.612 0.031 *
## OTU_3189 0.612 0.025 *
## OTU_3888 0.612 0.028 *
## OTU_4413 0.612 0.028 *
## OTU_5096 0.612 0.024 *
## OTU_5444 0.612 0.032 *
## OTU_5510 0.612 0.026 *
## OTU_6041 0.612 0.034 *
## OTU_6059 0.612 0.030 *
## OTU_6387 0.612 0.023 *
## OTU_6535 0.612 0.027 *
## OTU_6801 0.612 0.028 *
## OTU_8687 0.612 0.028 *
## OTU_8801 0.612 0.028 *
## OTU_8859 0.612 0.028 *
## OTU_9313 0.612 0.028 *
## OTU_9890 0.612 0.032 *
## OTU_10038 0.612 0.024 *
## OTU_10315 0.612 0.028 *
## OTU_10477 0.612 0.028 *
## OTU_10500 0.612 0.028 *
## OTU_10656 0.612 0.027 *
## OTU_11129 0.612 0.031 *
## OTU_11269 0.612 0.026 *
## OTU_11456 0.612 0.028 *
## OTU_11562 0.612 0.031 *
## OTU_11584 0.612 0.037 *
## OTU_11773 0.612 0.026 *
## OTU_12146 0.612 0.030 *
## OTU_12885 0.612 0.031 *
## OTU_13134 0.612 0.034 *
## OTU_13180 0.612 0.026 *
## OTU_13398 0.612 0.032 *
## OTU_1844 0.603 0.022 *
## OTU_11078 0.599 0.038 *
## OTU_1882 0.587 0.037 *
## OTU_7606 0.587 0.042 *
## OTU_8713 0.583 0.043 *
##
## Group Spinach #sps. 58
## stat p.value
## OTU_2655 1.000 0.001 ***
## OTU_4732 0.978 0.001 ***
## OTU_8281 0.972 0.001 ***
## OTU_1150 0.955 0.001 ***
## OTU_508 0.951 0.001 ***
## OTU_320 0.939 0.001 ***
## OTU_719 0.913 0.001 ***
## OTU_8799 0.886 0.001 ***
## OTU_1642 0.845 0.001 ***
## OTU_7290 0.845 0.001 ***
## OTU_13238 0.831 0.001 ***
## OTU_11334 0.823 0.001 ***
## OTU_4398 0.818 0.002 **
## OTU_10433 0.796 0.012 *
## OTU_10513 0.789 0.002 **
## OTU_12329 0.787 0.001 ***
## OTU_1618 0.778 0.002 **
## OTU_12015 0.773 0.001 ***
## OTU_3608 0.756 0.003 **
## OTU_7030 0.756 0.002 **
## OTU_9070 0.756 0.003 **
## OTU_11070 0.756 0.004 **
## OTU_12275 0.756 0.002 **
## OTU_9708 0.718 0.003 **
## OTU_7733 0.715 0.014 *
## OTU_5443 0.710 0.009 **
## OTU_2146 0.697 0.007 **
## OTU_1626 0.655 0.012 *
## OTU_2178 0.655 0.006 **
## OTU_2250 0.655 0.013 *
## OTU_3148 0.655 0.011 *
## OTU_3695 0.655 0.014 *
## OTU_3696 0.655 0.012 *
## OTU_5320 0.655 0.016 *
## OTU_5514 0.655 0.010 **
## OTU_5578 0.655 0.005 **
## OTU_7854 0.655 0.012 *
## OTU_9378 0.655 0.017 *
## OTU_10070 0.655 0.016 *
## OTU_11796 0.655 0.010 **
## OTU_10845 0.631 0.005 **
## OTU_3614 0.631 0.022 *
## OTU_6661 0.628 0.019 *
## OTU_1960 0.622 0.024 *
## OTU_2617 0.620 0.025 *
## OTU_7365 0.603 0.025 *
## OTU_367 0.535 0.050 *
## OTU_1821 0.535 0.044 *
## OTU_3843 0.535 0.043 *
## OTU_4741 0.535 0.045 *
## OTU_7297 0.535 0.050 *
## OTU_7881 0.535 0.043 *
## OTU_8958 0.535 0.043 *
## OTU_10494 0.535 0.050 *
## OTU_11077 0.535 0.050 *
## OTU_12457 0.535 0.050 *
## OTU_12665 0.535 0.050 *
## OTU_12730 0.535 0.045 *
##
## Group Strawberries #sps. 26
## stat p.value
## OTU_2080 0.784 0.003 **
## OTU_1763 0.781 0.011 *
## OTU_989 0.734 0.009 **
## OTU_3427 0.734 0.012 *
## OTU_4804 0.734 0.014 *
## OTU_7411 0.734 0.012 *
## OTU_5339 0.733 0.009 **
## OTU_10680 0.731 0.015 *
## OTU_10922 0.730 0.012 *
## OTU_9761 0.714 0.029 *
## OTU_2502 0.679 0.019 *
## OTU_4013 0.679 0.021 *
## OTU_4304 0.679 0.018 *
## OTU_6219 0.638 0.041 *
## OTU_6817 0.638 0.034 *
## OTU_13306 0.635 0.038 *
## OTU_6225 0.632 0.035 *
## OTU_370 0.620 0.024 *
## OTU_1683 0.620 0.048 *
## OTU_1689 0.620 0.031 *
## OTU_5122 0.620 0.035 *
## OTU_6276 0.620 0.037 *
## OTU_7337 0.620 0.036 *
## OTU_8990 0.620 0.034 *
## OTU_10876 0.620 0.041 *
## OTU_12316 0.620 0.035 *
##
## Group Mushrooms+Spinach #sps. 4
## stat p.value
## OTU_7240 0.997 0.001 ***
## OTU_13300 0.816 0.002 **
## OTU_5323 0.775 0.004 **
## OTU_5568 0.666 0.037 *
##
## Group Spinach+Strawberries #sps. 9
## stat p.value
## OTU_6975 0.996 0.001 ***
## OTU_6245 0.984 0.001 ***
## OTU_11811 0.952 0.001 ***
## OTU_64 0.894 0.001 ***
## OTU_1275 0.806 0.001 ***
## OTU_7928 0.806 0.002 **
## OTU_9230 0.707 0.033 *
## OTU_908 0.671 0.047 *
## OTU_13190 0.671 0.049 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1# Now lets use a custom function for plotting just 1 group indicators and choosing p value and indicator value cutoffs.
# Rerun the multipatt with the r.g func.
set.seed(1223) # For reproducibility
mp <- multipatt(t(input_filt_rar$data_loaded),
input_filt_rar$map_loaded$Sample_type,
func = "r.g",
control = how(nperm=999))
# This function was built with an 8th taxonomy column containing the ASV ID. Make here.
input_filt_rar$taxonomy_loaded$taxonomy8 <- rownames(input_filt_rar$taxonomy_loaded)
# It takes a summarized taxonomy dataframe, made like this.
tax_sum_asv <- summarize_taxonomy(input_filt_rar, level = 8, report_higher_tax = FALSE)
# The group must be a factor
input_filt_rar$map_loaded$Sample_type <- as.factor(input_filt_rar$map_loaded$Sample_type)
# Run the function.
plot_multipatt_asv(mp_obj = mp,
input = input_filt_rar,
tax_sum = tax_sum_asv,
group = "Sample_type",
filter = FALSE,
abund = "% Rel. Abund.",
qcut = 0.05, # Adjusted p value< 0.05
rcut = 0.5) # Can change r cutoff to be more or less selective
# This will plot the ASVs that passed the cutoffs. It will plot how correlated they are with a group as well as their % relative abundance. It will state the phylum and ASV ID.OTU/ASV Specific functions
# Let's look at the top taxa across samples (Can change the number you want seen)
return_top_taxa(input = input_filt_rar, number_taxa = 10)## taxonomy1 taxonomy2 taxonomy3
## OTU_6975 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
## OTU_5339 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
## OTU_1763 k__Bacteria p__Firmicutes c__Bacilli
## OTU_6245 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
## OTU_7240 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
## OTU_8870 k__Bacteria p__Bacteroidetes c__Flavobacteriia
## OTU_9155 k__Bacteria p__Bacteroidetes c__Sphingobacteriia
## OTU_10680 k__Bacteria p__Proteobacteria c__Alphaproteobacteria
## OTU_5927 k__Bacteria p__Bacteroidetes c__Sphingobacteriia
## OTU_320 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
## taxonomy4 taxonomy5 taxonomy6
## OTU_6975 o__Enterobacteriales f__Enterobacteriaceae g__Erwinia
## OTU_5339 o__Enterobacteriales f__Enterobacteriaceae g__Buchnera
## OTU_1763 o__Bacillales f__Bacillaceae g__
## OTU_6245 o__Enterobacteriales f__Enterobacteriaceae g__
## OTU_7240 o__Pseudomonadales f__Pseudomonadaceae g__Pseudomonas
## OTU_8870 o__Flavobacteriales f__[Weeksellaceae] g__Chryseobacterium
## OTU_9155 o__Sphingobacteriales f__Sphingobacteriaceae g__Pedobacter
## OTU_10680 o__Sphingomonadales f__Sphingomonadaceae g__Sphingomonas
## OTU_5927 o__Sphingobacteriales f__Sphingobacteriaceae g__Sphingobacterium
## OTU_320 o__Enterobacteriales f__Enterobacteriaceae g__Erwinia
## taxonomy7 taxonomy8
## OTU_6975 s__ OTU_6975
## OTU_5339 s__ OTU_5339
## OTU_1763 s__ OTU_1763
## OTU_6245 s__ OTU_6245
## OTU_7240 s__ OTU_7240
## OTU_8870 s__ OTU_8870
## OTU_9155 s__ OTU_9155
## OTU_10680 s__ OTU_10680
## OTU_5927 s__faecium OTU_5927
## OTU_320 s__ OTU_320# Calculates the top taxa based on number of counts - taking the row means for each OTU
# What taxa are common? Give them rarefied input, then level = "what level we want to summarize our information for". Check input_filt_rar$taxonomy_loaded for the levels. level 2 is phylum level
tax_sum_phyla <- summarize_taxonomy(input_filt_rar, level = 2, report_higher_tax = FALSE)
#level taxa=false- just look at that level, not at whole taxonomic classification
# How many phyla can we detect in this dataset
tax_sum_phyla## ProA12 ProA13 ProA14 ProA15 ProA16
## p__[Thermi] 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Actinobacteria 0.413066386 0.006322445 0.002107482 0.023182297 0.003161222
## p__Armatimonadetes 0.000000000 0.000000000 0.000000000 0.001053741 0.000000000
## p__Bacteroidetes 0.102212856 0.576396207 0.871443625 0.405690200 0.622760801
## p__Chlamydiae 0.000000000 0.000000000 0.000000000 0.003161222 0.000000000
## p__Chloroflexi 0.000000000 0.000000000 0.000000000 0.038988409 0.000000000
## p__Firmicutes 0.116965227 0.004214963 0.001053741 0.004214963 0.000000000
## p__Gemmatimonadetes 0.001053741 0.000000000 0.001053741 0.000000000 0.000000000
## p__Proteobacteria 0.365648051 0.413066386 0.124341412 0.523709168 0.374077977
## p__Tenericutes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__TM7 0.001053741 0.000000000 0.000000000 0.000000000 0.000000000
## ProA33 ProA34 ProA35 ProA36 ProA37
## p__[Thermi] 0.000000000 0.006322445 0.000000000 0.006322445 0.000000000
## p__Actinobacteria 0.042149631 0.066385669 0.094836670 0.027397260 0.002107482
## p__Armatimonadetes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Bacteroidetes 0.001053741 0.001053741 0.002107482 0.000000000 0.005268704
## p__Chlamydiae 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Chloroflexi 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Firmicutes 0.266596417 0.434141201 0.378292940 0.353003161 0.003161222
## p__Gemmatimonadetes 0.002107482 0.000000000 0.000000000 0.000000000 0.000000000
## p__Proteobacteria 0.688092729 0.489989463 0.524762908 0.611169652 0.989462592
## p__Tenericutes 0.000000000 0.000000000 0.000000000 0.002107482 0.000000000
## p__TM7 0.000000000 0.002107482 0.000000000 0.000000000 0.000000000
## ProA65 ProA66 ProB10 ProB12 ProB33
## p__[Thermi] 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
## p__Actinobacteria 0.002107482 0.006322445 0.02107482 0.005268704 0.007376185
## p__Armatimonadetes 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
## p__Bacteroidetes 0.005268704 0.001053741 0.39409905 0.547945205 0.006322445
## p__Chlamydiae 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
## p__Chloroflexi 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
## p__Firmicutes 0.041095890 0.068493151 0.02318230 0.024236038 0.007376185
## p__Gemmatimonadetes 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
## p__Proteobacteria 0.951527924 0.924130664 0.56164384 0.422550053 0.978925184
## p__Tenericutes 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
## p__TM7 0.000000000 0.000000000 0.00000000 0.000000000 0.000000000
## ProB34 ProB35 ProB36 ProB39 ProB40
## p__[Thermi] 0.001053741 0.000000000 0.000000000 0.000000000 0.000000000
## p__Actinobacteria 0.004214963 0.001053741 0.005268704 0.002107482 0.000000000
## p__Armatimonadetes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Bacteroidetes 0.000000000 0.000000000 0.000000000 0.011591149 0.000000000
## p__Chlamydiae 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Chloroflexi 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Firmicutes 0.022128556 0.001053741 0.003161222 0.021074816 0.009483667
## p__Gemmatimonadetes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Proteobacteria 0.972602740 0.997892518 0.991570074 0.965226554 0.990516333
## p__Tenericutes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__TM7 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## ProB67 ProB70 ProB71 ProB9 ProC36
## p__[Thermi] 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Actinobacteria 0.002107482 0.011591149 0.004214963 0.007376185 0.051633298
## p__Armatimonadetes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Bacteroidetes 0.011591149 0.007376185 0.007376185 0.197049526 0.004214963
## p__Chlamydiae 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Chloroflexi 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Firmicutes 0.066385669 0.128556375 0.167544784 0.092729189 0.054794521
## p__Gemmatimonadetes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__Proteobacteria 0.919915701 0.852476291 0.820864067 0.702845100 0.889357218
## p__Tenericutes 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## p__TM7 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
## ProC40 ProC65 ProC66
## p__[Thermi] 0.001053741 0.000000000 0.000000000
## p__Actinobacteria 0.013698630 0.002107482 0.004214963
## p__Armatimonadetes 0.000000000 0.000000000 0.000000000
## p__Bacteroidetes 0.002107482 0.000000000 0.000000000
## p__Chlamydiae 0.000000000 0.000000000 0.000000000
## p__Chloroflexi 0.000000000 0.000000000 0.000000000
## p__Firmicutes 0.790305585 0.008429926 0.007376185
## p__Gemmatimonadetes 0.000000000 0.000000000 0.000000000
## p__Proteobacteria 0.192834563 0.989462592 0.988408851
## p__Tenericutes 0.000000000 0.000000000 0.000000000
## p__TM7 0.000000000 0.000000000 0.000000000# Give most abundant phyla across dataset
tax_sum_phyla_Means <- sort(rowMeans(tax_sum_phyla), decreasing = T)
tax_sum_phyla_Means[1:5]## p__Proteobacteria p__Bacteroidetes p__Firmicutes p__Actinobacteria
## 0.722038236 0.135142255 0.110680415 0.029730543
## p__Chloroflexi
## 0.001392443# Now lets try summarizing at the family level (level 5)
tax_sum_families <- summarize_taxonomy(input_filt_rar, level = 5, report_higher_tax = FALSE)
head(tax_sum_families)## ProA12 ProA13 ProA14 ProA15
## f__ 0.012644889 0.002107482 0.001053741 0.038988409
## f__[Chromatiaceae] 0.002107482 0.000000000 0.000000000 0.002107482
## f__[Exiguobacteraceae] 0.053740780 0.002107482 0.000000000 0.000000000
## f__[Fimbriimonadaceae] 0.000000000 0.000000000 0.000000000 0.001053741
## f__[Weeksellaceae] 0.010537408 0.081138040 0.516332982 0.005268704
## f__Acetobacteraceae 0.000000000 0.000000000 0.000000000 0.000000000
## ProA16 ProA33 ProA34 ProA35
## f__ 0.0000000 0.008429926 0.002107482 0.002107482
## f__[Chromatiaceae] 0.0000000 0.000000000 0.000000000 0.000000000
## f__[Exiguobacteraceae] 0.0000000 0.000000000 0.000000000 0.000000000
## f__[Fimbriimonadaceae] 0.0000000 0.000000000 0.000000000 0.000000000
## f__[Weeksellaceae] 0.1928346 0.001053741 0.000000000 0.001053741
## f__Acetobacteraceae 0.0000000 0.022128556 0.001053741 0.000000000
## ProA36 ProA37 ProA65 ProA66 ProB10
## f__ 0.002107482 0 0.000000000 0.000000000 0.014752371
## f__[Chromatiaceae] 0.000000000 0 0.000000000 0.000000000 0.005268704
## f__[Exiguobacteraceae] 0.000000000 0 0.033719705 0.051633298 0.007376185
## f__[Fimbriimonadaceae] 0.000000000 0 0.000000000 0.000000000 0.000000000
## f__[Weeksellaceae] 0.000000000 0 0.003161222 0.001053741 0.106427819
## f__Acetobacteraceae 0.000000000 0 0.000000000 0.000000000 0.000000000
## ProB12 ProB33 ProB34 ProB35
## f__ 0.006322445 0.000000000 0.00000000 0.000000000
## f__[Chromatiaceae] 0.053740780 0.001053741 0.00000000 0.000000000
## f__[Exiguobacteraceae] 0.012644889 0.000000000 0.00000000 0.000000000
## f__[Fimbriimonadaceae] 0.000000000 0.000000000 0.00000000 0.000000000
## f__[Weeksellaceae] 0.011591149 0.002107482 0.00000000 0.000000000
## f__Acetobacteraceae 0.000000000 0.028451001 0.02212856 0.006322445
## ProB36 ProB39 ProB40 ProB67
## f__ 0.00000000 0.00000000 0.000000000 0.000000000
## f__[Chromatiaceae] 0.00000000 0.00000000 0.000000000 0.000000000
## f__[Exiguobacteraceae] 0.00000000 0.00000000 0.000000000 0.027397260
## f__[Fimbriimonadaceae] 0.00000000 0.00000000 0.000000000 0.000000000
## f__[Weeksellaceae] 0.00000000 0.01159115 0.000000000 0.002107482
## f__Acetobacteraceae 0.01791359 0.00000000 0.001053741 0.000000000
## ProB70 ProB71 ProB9 ProC36
## f__ 0.002107482 0.000000000 0.004214963 0.004214963
## f__[Chromatiaceae] 0.000000000 0.000000000 0.024236038 0.000000000
## f__[Exiguobacteraceae] 0.057955743 0.061116965 0.068493151 0.002107482
## f__[Fimbriimonadaceae] 0.000000000 0.000000000 0.000000000 0.000000000
## f__[Weeksellaceae] 0.003161222 0.003161222 0.024236038 0.000000000
## f__Acetobacteraceae 0.000000000 0.000000000 0.000000000 0.000000000
## ProC40 ProC65 ProC66
## f__ 0.001053741 0.000000000 0.000000000
## f__[Chromatiaceae] 0.000000000 0.000000000 0.000000000
## f__[Exiguobacteraceae] 0.000000000 0.005268704 0.002107482
## f__[Fimbriimonadaceae] 0.000000000 0.000000000 0.000000000
## f__[Weeksellaceae] 0.000000000 0.000000000 0.000000000
## f__Acetobacteraceae 0.000000000 0.000000000 0.000000000Other useful plotting and analysis functions
Base mctoolsR has some other nice functions for running statistical tests on taxonomic abundances as well as plotting heatmaps and stacked bar plots. We also demonstrate some customizations on the base functions. For more information on mctoolsR functions, see the tutorial at https://github.com/leffj/mctoolsr.
# Summarize at family level. Choose different levels with the level argument
tax_sum_families <- summarize_taxonomy(input_filt_rar, level = 5, report_higher_tax = FALSE)
# Default heatmap
plot_ts_heatmap(tax_sum_families,
input_filt_rar$map_loaded,
0.01,
'Sample_type')## Warning: `mutate_()` was deprecated in dplyr 0.7.0.
## ℹ Please use `mutate()` instead.
## ℹ See vignette('programming') for more help
## ℹ The deprecated feature was likely used in the mctoolsr package.
## Please report the issue at <https://github.com/leffj/mctoolsr/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Add some customization
plot_ts_heatmap(tax_sum_families,
input_filt_rar$map_loaded,
0.01,
'Sample_type',
rev_taxa = T) +
coord_flip() +
theme(axis.text.x = element_text(size = 12, angle = 45, vjust = 1))
# Default (choose how many taxa you want with num_taxa)
plot_taxa_bars(tax_sum_families,
input_filt_rar$map_loaded,
"Sample_type",
num_taxa = 10)## Warning: `summarise_()` was deprecated in dplyr 0.7.0.
## ℹ Please use `summarise()` instead.
## ℹ The deprecated feature was likely used in the mctoolsr package.
## Please report the issue at <https://github.com/leffj/mctoolsr/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Add some customization
plot_taxa_bars(tax_sum_families,
input_filt_rar$map_loaded,
"Sample_type",
num_taxa = 10) +
labs(x = "Sample Type", y = "Relative Abundance", fill = "Family") +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
# Add even more customization. plot_taxa_bars has a data_only argument. So you can save the dataset created and then write your own plot!
bars <- plot_taxa_bars(tax_sum_families,
input_filt_rar$map_loaded,
"Sample_type",
num_taxa = 10,
data_only = TRUE)
ggplot(bars, aes(group_by, mean_value, fill = taxon)) +
geom_bar(stat = "identity", colour = "black", linewidth = 0.25) +
labs(x = "Sample Type", y = "Relative Abundance", fill = "Family") +
scale_fill_brewer(palette = "Paired") +
theme_bw() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
# Different style - classic theme, no black lines between taxa.
ggplot(bars, aes(group_by, mean_value, fill = taxon)) +
geom_bar(stat = "identity", linewidth = 0.25) +
labs(x = "Sample Type", y = "Relative Abundance", fill = "Family") +
scale_fill_brewer(palette = "Paired") +
theme_classic() +
theme(axis.title = element_text(face = "bold", size = 16),
axis.text = element_text(size = 14))
# Now try a cliffplot! This is a custom function by Cliff Bueno de Mesquita that serves as a nice but quick overview of the top taxa at different levels. The function is in the GitHub repository and was imported with the source() function in the setup portion of this tutorial. You can ignore the warnings, which have to do with whether or not unclassified taxa were in the top 12 of a particular taxonomic level. It was also made with a SILVA version that writes Unclassified instead of unclassified.
cliffplot_taxa_bars(input = input_filt_rar, level = 1, variable = "Sample_type")## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
cliffplot_taxa_bars(input = input_filt_rar, level = 2, variable = "Sample_type")
cliffplot_taxa_bars(input = input_filt_rar, level = 3, variable = "Sample_type")## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `taxon = fct_relevel(taxon, "Unclassified", after = Inf)`.
## ℹ In group 1: `group_by = Mushrooms`.
## Caused by warning:
## ! 1 unknown level in `f`: Unclassified
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.
cliffplot_taxa_bars(input = input_filt_rar, level = 4, variable = "Sample_type")## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `taxon = fct_relevel(taxon, "Unclassified", after = Inf)`.
## ℹ In group 1: `group_by = Mushrooms`.
## Caused by warning:
## ! 1 unknown level in `f`: Unclassified
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.
cliffplot_taxa_bars(input = input_filt_rar, level = 5, variable = "Sample_type")## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `taxon = fct_relevel(taxon, "Unclassified", after = Inf)`.
## ℹ In group 1: `group_by = Mushrooms`.
## Caused by warning:
## ! 1 unknown level in `f`: Unclassified
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.
cliffplot_taxa_bars(input = input_filt_rar, level = 6, variable = "Sample_type")## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `taxon = fct_relevel(taxon, "Unclassified", after = Inf)`.
## ℹ In group 1: `group_by = Mushrooms`.
## Caused by warning:
## ! 1 unknown level in `f`: Unclassified
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.
cliffplot_taxa_bars(input = input_filt_rar, level = 7, variable = "Sample_type")## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `taxon = fct_relevel(taxon, "Unclassified", after = Inf)`.
## ℹ In group 1: `group_by = Mushrooms`.
## Caused by warning:
## ! 1 unknown level in `f`: Unclassified
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.
cliffplot_taxa_bars(input = input_filt_rar, level = 8, variable = "Sample_type")## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `taxon = fct_relevel(taxon, "Unclassified", after = Inf)`.
## ℹ In group 1: `group_by = Mushrooms`.
## Caused by warning:
## ! 1 unknown level in `f`: Unclassified
## ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.
# Add even more customization. Try a nested facet! These are great for parsing your taxonomy plot by different grouping variables. Set the sampleID as the grouping variable so a bar is made for each sample. Utilize the nested facets to show the differences among the actual grouping variables.
# Make sampleID column
input_filt_rar$map_loaded$sampleID <- rownames(input_filt_rar$map_loaded)
# Summarize taxonomy. Let's do families.
tax_sum_families <- summarize_taxonomy(input_filt_rar, level = 5, report_higher_tax = FALSE)
# Get the plotting data. We'll also join the rest of map_loaded.
bars <- plot_taxa_bars(tax_sum_families,
input_filt_rar$map_loaded,
"sampleID",
num_taxa = 12,
data_only = TRUE) %>%
mutate(taxon = fct_rev(taxon)) %>%
left_join(., input_filt_rar$map_loaded, by = c("group_by" = "sampleID"))
# Run stats and add an asterisk to their name in the legend if significantly affected by treatment
fam_stats <- taxa_summary_by_sample_type(tax_sum_families,
input_filt_rar$map_loaded,
type_header = 'Sample_type',
filter_level = 0.01,
test_type = 'KW') %>%
filter(rownames(.) %in% bars$taxon) %>%
arrange(desc(rownames(.))) %>%
mutate(Sig = ifelse(pvalsFDR < 0.05, "Pfdr < 0.05", "Pfdr > 0.05")) %>%
mutate(Star = ifelse(pvalsFDR < 0.05, "*", "")) %>%
rownames_to_column(var = "taxon") %>%
arrange(match(taxon, levels(bars$taxon))) %>%
mutate(StarLab = paste(taxon, Star, sep = " "))
# Plot
ggplot(bars, aes(group_by, mean_value, fill = taxon)) +
geom_bar(stat = "identity", linewidth = 0.25) +
labs(x = "Sample Type", y = "Relative Abundance", fill = "Family") +
scale_fill_manual(values = c("grey90", brewer.pal(12, "Paired")[12:1]),
labels = c("Other", fam_stats$StarLab)) +
scale_y_continuous(expand = c(0.01, 0.01)) +
facet_nested(~ Farm_type + Sample_type, space = "free", scales = "free_x") +
theme_classic() +
theme(axis.title.y = element_text(face = "bold", size = 12),
axis.title.x = element_blank(),
axis.text.y = element_text(size = 10),
axis.text.x = element_text(size = 8, angle = 90, hjust = 1, vjust = 0.5),
axis.ticks.x = element_blank(),
axis.line.x = element_blank(),
strip.text = element_text(size = 6),
strip.background = element_rect(linewidth = 0.2),
axis.line.y = element_blank(),
legend.margin = margin(0, 0, 0, 0, unit = "pt"),
legend.box.margin = margin(0, 0, 0, 0, unit = "pt"),
legend.key.size = unit(0.3, "cm"),
panel.spacing.x = unit(c(0.2, 0.2, 0.4, 0.2, 0.2), "lines"))
# Test (run a Kruskal-Wallis test on all families with mean rel abund. > filter_level in at least one of the factor levels)
taxa_summary_by_sample_type(tax_sum_families,
input_filt_rar$map_loaded,
type_header = 'Sample_type',
filter_level = 0.05,
test_type = 'KW')## pvals pvalsBon pvalsFDR Mushrooms
## f__Pseudomonadaceae 1.462593e-05 0.0001170074 0.0001170074 0.162671233
## f__Sphingobacteriaceae 5.463909e-05 0.0004371127 0.0002185564 0.316122234
## f__[Weeksellaceae] 1.246078e-04 0.0009968628 0.0003322876 0.118545838
## f__Enterobacteriaceae 4.669735e-04 0.0037357879 0.0009339470 0.035958904
## f__Bacillaceae 1.761396e-02 0.1409117049 0.0281823410 0.002502634
## f__Oxalobacteraceae 6.710803e-02 0.5368642596 0.0894773766 0.050316122
## f__Sphingomonadaceae 7.023547e-02 0.5618837856 0.0802691122 0.007639621
## f__Micrococcaceae 5.776766e-01 4.6214126447 0.5776765806 0.052555321
## Spinach Strawberries
## f__Pseudomonadaceae 0.066084600 0.0014590257
## f__Sphingobacteriaceae 0.002258016 0.0004863419
## f__[Weeksellaceae] 0.001806413 0.0012158547
## f__Enterobacteriaceae 0.771940388 0.6403501662
## f__Bacillaceae 0.002709619 0.1703817784
## f__Oxalobacteraceae 0.012494355 0.0094026100
## f__Sphingomonadaceae 0.000752672 0.0594147686
## f__Micrococcaceae 0.001806413 0.0108616357# Or Wilcoxon for 2 levels (farm type)
taxa_summary_by_sample_type(tax_sum_families,
input_filt_rar$map_loaded,
type_header = 'Farm_type',
filter_level = 0.05,
test_type = 'MW')## Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...): cannot
## compute exact p-value with ties## Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...): cannot
## compute exact p-value with ties
## Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...): cannot
## compute exact p-value with ties## pvals pvalsBon pvalsFDR Conventional Organic
## f__[Weeksellaceae] 0.1246744 0.6233719 0.6233719 0.009073879 0.08134879
## f__Bacillaceae 0.1410588 0.7052939 0.3526469 0.079674511 0.08198103
## f__Sphingobacteriaceae 0.3120693 1.5603463 0.5201154 0.049994146 0.16512118
## f__Enterobacteriaceae 0.5330298 2.6651492 0.6662873 0.543730242 0.42286617
## f__Pseudomonadaceae 0.6118674 3.0593371 0.6118674 0.048823323 0.09041096